Here are some findings from my side. I have to remove
~/Library/Application Support/Sublime Text 3/Lib/python3.3
~/Library/Application Support/Sublime Text 3/Installed Packages/PyV8
both get re-created when I restart Sublime Text. When these are there, then the Preferences menu is greyed out. If I remove then and then start Sublime Text, I can access the Preferences menu, until, I quit Sublime Text and forget removing them.
So it has something to do with python, but I've no idea how.
Also, I've some packages installed, but besides the PyV8, which gets re-created, none of the others seem to hurt by themselves.